Objectives Preparation of 5-FU elastomeric pumps is a time-consuming activity inducing musculoskeletal disorders (MSDs). Our unit has developed an automated filling system consisting of two peristaltic pumps (one for the diluent, one for the cytotoxic drug). The objective was to validate the accuracy of the assembly and evaluate the impact of automation on the compounding time, occurrence of MSDs and cost of preparation. Methods Accuracy was determined by calculating the total error on the volumes injected by the pumps. Measurements were made for 2 brands (AMF, Baxter), 3 different volumes; repeated 3 times at 3 times of the day. The time-saving study compared 24 measurements in manual filling and 24 in automated mode. Impact of automation on the occurrence of MSDs was evaluated by a self-assessment questionnaire. Finally, a comparison between the price of a manually prepared elastomeric pump and an automated prepared elastomeric pump was performed. Results Volumes administered by the pumps were accurate (total error < 2.5%). Preparation time was divided by 2. Occurrence of MSD decreased (8.7 manual filling vs. 23.5/28 automated filling). Overcost was moderate (14.7% for AMF; 10.3% for Baxter). Conclusions Using peristaltic pumps, 5FU preparation was optimized for moderate additional cost.